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@book{goel,
	Author = {Goel, Narendra S. and Richter-Dyn, Nira},
	Date-Added = {2007-08-21 12:18:30 -0700},
	Date-Modified = {2007-08-21 12:19:07 -0700},
	Publisher = {Academic Press},
	Title = {Stochastic models in biology},
	Year = {1975}}

@article{muller,
	Author = {M{\"u}ller, Peter and West, Mike and Mac{E}achern, Steven},
	Date-Added = {2007-08-20 14:15:43 -0700},
	Date-Modified = {2007-08-20 14:16:38 -0700},
	Journal = {Journal of Time Series Analysis},
	Number = {6},
	Title = {Bayesian models for non-linear autoregressions},
	Volume = {18},
	Year = {1997}}

@article{requiem,
	Author = {Mangel, Marc and Marinovic, Baldo and Pomeroy, Caroline and Croll, Donald},
	Date-Added = {2007-08-20 13:00:13 -0700},
	Date-Modified = {2007-08-20 13:01:18 -0700},
	Journal = {Bulletin of marine science},
	Number = {2},
	Pages = {763-781},
	Title = {Requiem for {R}icker: unpacking {MSY}},
	Volume = {70},
	Year = {2002}}

@book{ricker,
	Address = {Ottawa, Ontario, Canada},
	Author = {Ricker, W. E.},
	Date-Added = {2007-08-20 12:58:17 -0700},
	Date-Modified = {2007-08-20 12:59:56 -0700},
	Number = {191},
	Publisher = {Department of Environment, Fisheries and Marine Service},
	Series = {Bulletin (Fisheries Reserves Board of Canada)},
	Title = {Computation and interpretation of biological statistics of fish populations},
	Year = {1975}}

@book{colored_noise,
	Author = {Horsthemke, W. and Lefever, R.},
	Date-Added = {2007-08-12 19:29:45 -0700},
	Date-Modified = {2007-08-12 19:31:02 -0700},
	Publisher = {Springer},
	Series = {Springer series in synergetics},
	Title = {Noise-induced transitions: applications in physics, chemistry and biology},
	Year = {1984}}

@book{williams,
	Author = {Rasmussen, C. E. and Williams, C. K. I.},
	Date-Added = {2007-08-09 15:30:46 -0700},
	Date-Modified = {2007-08-09 15:31:18 -0700},
	Publisher = {MIT Press},
	Title = {Gaussian processes for machine learning},
	Year = {2006}}

@book{ghosh_ramamoorthi,
	Author = {Ghosh, J. K. and Ramamoorthi, R. V.},
	Date-Added = {2007-08-09 15:09:00 -0700},
	Date-Modified = {2007-08-09 15:10:10 -0700},
	Publisher = {Springer},
	Title = {Bayesian nonparametrics},
	Year = {2003}}

@book{hilborn_walters,
	Author = {Hilborn, R. and Walters, C. J.},
	Date-Added = {2007-08-09 14:35:23 -0700},
	Date-Modified = {2007-08-09 14:48:44 -0700},
	Publisher = {Springer},
	Title = {Quantitative fisheries stock assessment: choice, dynamics and uncertainty},
	Year = {1991}}

@book{quinn_deriso,
	Author = {Quinn, Terrance J. and Deriso, Richard B.},
	Date-Added = {2007-08-09 14:33:07 -0700},
	Date-Modified = {2007-08-09 14:35:20 -0700},
	Publisher = {Oxford University Press},
	Title = {Quantitative fish dynamics},
	Year = {1999}}

@book{Kolchin,
	Author = {Kolchin, V. and Sewast'yanov, B. and Chistyakov, V.},
	Date-Added = {2007-07-31 12:47:01 -0700},
	Date-Modified = {2007-07-31 12:47:59 -0700},
	Publisher = {Wiley {\&} sons},
	Title = {Random allocations},
	Year = {1977}}

@incollection{maystability,
	Author = {May, Robert M.},
	Booktitle = {Landmarks in Biology},
	Date-Added = {2007-07-09 14:26:17 -0400},
	Date-Modified = {2007-07-09 14:27:22 -0400},
	Publisher = {Princeton University Press},
	Title = {Stability and complexity in model ecosystems},
	Year = {2001}}

@phdthesis{weisberg,
	Author = {Weisberg, Michael},
	Date-Added = {2007-07-02 14:13:43 -0400},
	Date-Modified = {2007-07-02 14:14:26 -0400},
	School = {Stanford University},
	Title = {When less is more: tradeoffs and idealization in model building},
	Year = {2003}}

@unpublished{beskos_langevin,
	Author = {Beskos, Alexandros and Roberts, Gareth O. and Stuart, Andrew M. and Voss, Jochen},
	Date-Added = {2007-07-02 11:43:56 -0400},
	Date-Modified = {2007-07-02 11:44:46 -0400},
	Note = {Available from url},
	Title = {An MCMC Method for Diffusion Bridges}}

@article{levins,
	Author = {Levins, Richard},
	Date-Added = {2007-06-30 20:23:29 -0400},
	Date-Modified = {2007-06-30 20:24:22 -0400},
	Journal = {American Scientist},
	Pages = {421-431},
	Title = {The strategy of model building in population biology},
	Volume = {54},
	Year = {1966}}

@book{jaynes,
	Author = {Jaynes, E. T.},
	Date-Added = {2007-06-30 18:12:47 -0400},
	Date-Modified = {2007-06-30 18:14:15 -0400},
	Publisher = {Cambridge University Press},
	Title = {Probability theory: the logic of science},
	Year = {2003}}

@article{cushing,
	Author = {Cushing, J. M. and Constantino, R. F. and Dennis, Brian and Desharnais, R. A. and Henson, Shandelle M.},
	Date-Added = {2007-06-30 18:10:25 -0400},
	Date-Modified = {2007-06-30 18:11:32 -0400},
	Journal = {Journal of Theoretical Biology},
	Pages = {1-9},
	Title = {Nonlinear population dynamics: models, experiments and data},
	Volume = {194},
	Year = {1998}}

@book{fortran,
	Author = {Nyhoff, Larry and Leestma, Sanford},
	Date-Added = {2007-06-29 13:46:26 -0700},
	Date-Modified = {2007-06-29 13:47:32 -0700},
	Edition = {4th},
	Publisher = {Prentice-Hall, Inc.},
	Title = {{FORTRAN} 77 for engineers and scientists with an introduction to {FORTRAN} 90},
	Year = {1995}}

@techreport{abrahamsen,
	Author = {Abrahamsen, Petter},
	Date-Added = {2007-06-29 12:33:35 -0700},
	Date-Modified = {2007-06-29 12:35:26 -0700},
	Institution = {Norwegian Computing Center},
	Number = {917},
	Title = {A review of {G}aussian random fields and correlation functions},
	Year = {1997}}

@book{ockendon,
	Author = {Ockendon, Hilary},
	Date-Added = {2007-06-29 12:24:59 -0700},
	Date-Modified = {2007-06-29 14:27:06 -0700},
	Publisher = {Cambridge University Press},
	Title = {Viscous flow},
	Year = {1995}}

@article{lang_pspline,
	Author = {Lang, Stefan and Brezger, Andreas},
	Date-Added = {2007-06-29 11:40:07 -0700},
	Date-Modified = {2007-06-29 11:41:29 -0700},
	Journal = {Journal of Computational and Graphical Statistics},
	Number = {1},
	Pages = {183-212},
	Title = {Bayesian {P}-splines},
	Volume = {13},
	Year = {2004}}

@book{micula,
	Author = {Micula, Georghe and Micula, Sanda},
	Date-Added = {2007-06-29 11:39:23 -0700},
	Date-Modified = {2007-06-29 11:40:06 -0700},
	Publisher = {Kluwer Academic},
	Title = {Handbook of Splines},
	Year = {1999}}

@incollection{heesterbeek,
	Author = {Heesterbeek, Hans},
	Booktitle = {Ecological paradigms lost: routes of theory change},
	Chapter = {5},
	Date-Added = {2007-06-29 10:09:14 -0700},
	Date-Modified = {2007-06-29 10:13:06 -0700},
	Editor = {Cuddington, Kim and Beisner, Beatrix},
	Publisher = {Elsevier Academic Press},
	Title = {The law of mass-action in epidemiology: a historical perspective},
	Year = {2005}}

@incollection{hastings,
	Author = {Hastings, Alan},
	Booktitle = {Ecological paradigms lost: routes of theory change},
	Chapter = {2},
	Date-Added = {2007-06-29 10:09:12 -0700},
	Date-Modified = {2007-06-29 10:12:56 -0700},
	Editor = {Cuddington, Kim and Beisner, Beatrix},
	Publisher = {Elsevier Academic Press},
	Title = {Unstructured models in ecology: past, present, and future},
	Year = {2005}}

@article{Ellner97,
	Author = {Ellner, S. P.},
	Date-Added = {2007-06-28 21:26:49 -0700},
	Date-Modified = {2007-06-28 21:26:49 -0700},
	Journal = {Physica D.},
	Pages = {182-194},
	Title = {Inferring mechanism from time-series data: Delay-differential equations},
	Volume = {110},
	Year = {1997}}

@incollection{deroos,
	Author = {De{R}oos, Andr{\'e} M. and Persson, Lennart},
	Booktitle = {Ecological paradigms lost: routes of theory change},
	Date-Added = {2007-06-28 18:44:00 -0700},
	Date-Modified = {2007-06-29 10:13:54 -0700},
	Editor = {Cuddington, Kim and Beisner, Beatrix},
	Publisher = {Elsevier Academic Press},
	Title = {Unstructured population models: do population-level assumptions yield general theory?},
	Year = {2005}}

@article{mckendrick,
	Author = {McKendrick, A. G.},
	Date-Added = {2007-06-28 18:40:47 -0700},
	Date-Modified = {2007-06-28 18:42:35 -0700},
	Journal = {Paludism (Transactions of the Committee for the Study of Malaria in India)},
	Pages = {54-66},
	Title = {The rise and fall of epidemics.},
	Volume = {1},
	Year = {1912}}

@article{hamer,
	Author = {Hamer, W. H.},
	Date-Added = {2007-06-28 18:39:46 -0700},
	Date-Modified = {2007-06-28 18:40:45 -0700},
	Journal = {Transactions of the Epidemiological Society of London},
	Pages = {64-77},
	Title = {Age-incidence in relation with cycles of disease prevalence.},
	Volume = {16},
	Year = {1896}}

@book{spencer,
	Author = {Spencer, Herbert},
	Date-Added = {2007-06-28 15:02:12 -0700},
	Date-Modified = {2007-06-29 14:27:53 -0700},
	Edition = {3rd},
	Publisher = {D. Appleton},
	Title = {Principles of psychology},
	Year = {1902}}

@article{lotka_econ,
	Author = {Lotka, Alfred J.},
	Date-Added = {2007-06-28 15:01:02 -0700},
	Date-Modified = {2007-06-28 15:02:06 -0700},
	Journal = {Journal of the Washington Academy of Sciences},
	Pages = {409-418, 447-457, 499-500},
	Title = {An objective standard of value derived from the principle of evolution},
	Volume = {4},
	Year = {1914}}

@incollection{lelech9,
	Author = {Taper, Mark L. and Lele, Subhash R.},
	Booktitle = {The nature of scientific evidence},
	Date-Added = {2007-06-28 14:59:01 -0700},
	Date-Modified = {2007-06-28 15:00:34 -0700},
	Editor = {Taper, Mark L. and Lele, Subhash R.},
	Publisher = {The University of Chicago Press},
	Title = {Dynamical models as paths to evidence in ecology},
	Year = {2004}}

@article{green,
	Author = {Green, P. J.},
	Date-Added = {2007-06-21 21:18:51 -0700},
	Date-Modified = {2007-06-29 14:18:13 -0700},
	Journal = {Biometrika},
	Title = {Reversible jump {M}arkov chain {M}onte {C}arlo computation and {B}ayesian model determination},
	Year = {1995}}

@book{gilks,
	Date-Added = {2007-06-21 15:55:43 -0700},
	Date-Modified = {2007-06-21 16:01:10 -0700},
	Editor = {Gilks, W. R. and Richardson, S. and Spiegelhalter, D.},
	Publisher = {Chapman {\&} Hall {/} CRC},
	Title = {Markov chain Monte Carlo in practice},
	Year = {1995}}

@unpublished{Seeger,
	Author = {Seeger, Matthias},
	Date-Added = {2007-06-19 21:51:28 -0700},
	Date-Modified = {2007-06-19 21:53:13 -0700},
	Note = {Available from http://www.kyb.tuebingen.mpg.de/bs/people/seeger/papers/cholupdate.pdf},
	Title = {Low rank updates for the {C}holesky decomposition}}

@book{Linpack,
	Author = {Dongarra, J. J. and Moler, C. B. and Bunch, J. R. and Stewart, G. W.},
	Date-Added = {2007-06-19 21:49:15 -0700},
	Date-Modified = {2007-06-19 21:50:49 -0700},
	Publisher = {SIAM},
	Title = {Linpack user's guide},
	Year = {1979}}

@book{golub,
	Author = {Golub, Gene H. and {v}an Loan, Charles F.},
	Date-Added = {2007-06-19 21:47:47 -0700},
	Date-Modified = {2007-06-19 21:49:04 -0700},
	Edition = {third},
	Publisher = {The Johns Hopkins University Press},
	Title = {Matrix computations},
	Year = {1996}}

@unpublished{me_SR,
	Author = {Patil, Anand},
	Date-Added = {2007-06-19 21:31:11 -0700},
	Date-Modified = {2007-06-28 21:30:59 -0700},
	Note = {Available from http://code.google.com/p/gaussian-process},
	Title = {Random {R}ealizations user's guide}}

@article{OOP_review,
	Author = {Armstrong, Deborah J.},
	Date-Added = {2007-06-17 20:22:10 -0700},
	Date-Modified = {2007-06-17 20:22:53 -0700},
	Journal = {Communications of the ACM},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/PyMC/OOP_review.pdf},
	Number = {2},
	Title = {The Quarks of Object-Oriented Development},
	Volume = {49},
	Year = {2006}}

@article{silvert_OOP,
	Author = {Silvert, William},
	Date-Added = {2007-06-17 20:21:12 -0700},
	Date-Modified = {2007-06-17 20:21:50 -0700},
	Journal = {Ecological Modelling},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/PyMC/silvert_OOP.pdf},
	Pages = {91-118},
	Title = {Object-oriented ecosystem modelling},
	Year = {1993}}

@book{spanos,
	Author = {Ghanem, Roger G. and Spanos, Pol D.},
	Date-Added = {2007-06-17 17:23:32 -0700},
	Date-Modified = {2007-06-17 17:23:32 -0700},
	Publisher = {Dover Publications},
	Title = {Stochastic finite elements: a spectral approach},
	Year = {1991}}

@article{convolution,
	Author = {Lee, Herbert K. H. and Higdon, Dave M. and Calder, Catherine A. and Holloman, Christopher H.},
	Date-Added = {2007-06-17 17:23:32 -0700},
	Date-Modified = {2007-06-17 17:23:32 -0700},
	Journal = {Statistical Modelling},
	Number = {1},
	Pages = {53-74},
	Title = {Efficient models for correlated data via convolutions of intrinsic processes},
	Volume = {5},
	Year = {2005}}

@book{neuro,
	Author = {Levitan, Irwin B. and Kaczmarek, Leonard K.},
	Date-Added = {2007-06-17 17:23:32 -0700},
	Date-Modified = {2007-06-17 17:23:32 -0700},
	Publisher = {Oxford University Press},
	Title = {The neuron: cell and molecular biology},
	Year = {1997}}

@book{fraccalc,
	Author = {Miller, Kenneth S. and Ross, Betram},
	Date-Added = {2007-06-17 17:23:32 -0700},
	Date-Modified = {2007-06-17 17:23:32 -0700},
	Publisher = {John Wiley and Sons},
	Title = {An introduction to the fractional calculus and fractional differential equations},
	Year = {1993}}

@book{microecon,
	Author = {Nicholson, Walter},
	Date-Added = {2007-06-17 17:23:32 -0700},
	Date-Modified = {2007-06-17 17:23:32 -0700},
	Edition = {Eighth},
	Publisher = {Thomson Learning},
	Title = {Microeconomic Theory},
	Year = {2002}}

@book{numpybook,
	Author = {Oliphant, Travis E.},
	Date-Added = {2007-06-17 17:23:32 -0700},
	Date-Modified = {2007-06-17 17:23:32 -0700},
	Publisher = {Trelgol Publishing},
	Title = {Guide to NumPy},
	Year = {2006}}

@inproceedings{pachische,
	Author = {Paciorek, Christopher J. and Schervish, Mark J.},
	Booktitle = {NIPS conference proceedings},
	Date-Added = {2007-06-17 17:23:32 -0700},
	Date-Modified = {2007-06-17 17:23:32 -0700},
	Title = {Nonstationary covariance functions for Gaussian process regression},
	Year = {2004}}

@book{rudin,
	Author = {Rudin, Walter},
	Date-Added = {2007-06-17 17:23:32 -0700},
	Date-Modified = {2007-06-17 17:23:32 -0700},
	Publisher = {McGraw-Hill},
	Title = {Real {\&} complex analysis},
	Year = {1966}}

@article{sampson,
	Author = {Sampson, P. D. and Guttorp, Peter},
	Date-Added = {2007-06-17 17:23:32 -0700},
	Date-Modified = {2007-06-17 17:23:32 -0700},
	Journal = {Journal of the American Statistical Association},
	Number = {417},
	Pages = {108-119},
	Title = {Nonparametric estimation of nonstationary spatial covariance structure},
	Volume = {87},
	Year = {1992}}

@book{mathecol,
	Author = {Vandermeer, John H.},
	Date-Added = {2007-06-17 17:23:32 -0700},
	Date-Modified = {2007-06-17 17:23:32 -0700},
	Publisher = {Krieger Publication Co.},
	Title = {Elementary mathematical ecology},
	Year = {1990}}

@book{berry,
	Author = {Berry, Donald A.},
	Date-Added = {2007-06-17 17:22:38 -0700},
	Date-Modified = {2007-06-17 17:22:38 -0700},
	Publisher = {Duxbury Press},
	Title = {Statistics: a Bayesian perspective},
	Year = {1996}}

@book{diggle,
	Author = {Diggle, Peter J. and Ribeiro, Paulo J.},
	Date-Added = {2007-06-17 17:22:38 -0700},
	Date-Modified = {2007-06-17 17:22:38 -0700},
	Publisher = {Springer},
	Title = {Model-based geostatistics},
	Year = {2007}}

@book{duffy,
	Author = {Duffy, Dean G.},
	Date-Added = {2007-06-17 17:22:38 -0700},
	Date-Modified = {2007-06-17 17:22:39 -0700},
	Publisher = {CRC Press},
	Title = {Advanced Engineering Mathematics},
	Year = {1997}}

@article{incompchol,
	Author = {Fine, Shai and Scheinberg, Katya},
	Date-Added = {2007-06-17 17:22:38 -0700},
	Date-Modified = {2007-06-29 14:17:40 -0700},
	Journal = {Journal of Machine Learning Research},
	Pages = {243-264},
	Title = {Efficient {SVM} training using low-rank kernel representations},
	Volume = {2},
	Year = {2001}}

@book{andersonmay,
	Author = {Anderson, Roy M. and May, Robeert M.},
	Date-Added = {2007-06-17 17:22:17 -0700},
	Date-Modified = {2007-06-17 17:22:17 -0700},
	Publisher = {Oxford Science Publications},
	Title = {Infectious diseases of humans: dynamics and control},
	Year = {1992}}

@inproceedings{predictivechol,
	Author = {Bach, Francis R. and Jordan, Michael I.},
	Booktitle = {Proceedings of the 22nd International Conference on Machine learning},
	Date-Added = {2007-06-17 17:22:17 -0700},
	Date-Modified = {2007-06-17 17:22:17 -0700},
	Title = {Predictive low-rank decomposition for kernel methods},
	Year = {2005}}

@article{may,
	Author = {May, Robert M. and Beddington, J. R. and Horwood, J. W. and Shepherd, J. G.},
	Date-Added = {2007-06-17 00:11:55 -0700},
	Date-Modified = {2007-06-17 00:13:34 -0700},
	Journal = {Mathematical Biosciences},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/rockfish_DLM/may.pdf},
	Pages = {219-252},
	Title = {Exploiting natural populations in an uncertain world},
	Volume = {42},
	Year = {1978}}

@article{hollowed,
	Author = {Hollowed, Anne B. and Bax, Nicholas and Beamish, Richard and Collie, Jeremy and Fogarty, Michael and Livingston, Patricia and Pope, John and Rice, Jake C.},
	Date-Added = {2007-06-16 23:58:08 -0700},
	Date-Modified = {2007-06-16 23:59:33 -0700},
	Journal = {ICES Journal of Marine Science},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/rockfish_DLM/hollowed.pdf},
	Pages = {707-719},
	Title = {Are multispecies models an improvement on single-species models for measuring fishing impacts on marine ecosystems?},
	Volume = {57},
	Year = {2000}}

@techreport{caddy_mahon,
	Author = {Caddy, J. F. and Mahon. R.},
	Date-Added = {2007-06-16 23:14:58 -0700},
	Date-Modified = {2007-06-16 23:15:48 -0700},
	Institution = {FAO},
	Number = {347},
	Title = {Reference points for fishery management},
	Type = {Fisheries Technical Paper},
	Year = {1995}}

@article{caddy_refpoint,
	Annote = {About invertebrates.

LRP is limit reference point. UN Fish Stock Agreement and FAO Code of Conduct for Responsible Fisheries 'highlighted' the use of LRP's.

Reflects a growing appreciation of the low precision possible in determining resource status and hence the risks of overshooting targets.

Ehh... too many words.},
	Author = {Caddy, J. F.},
	Date-Added = {2007-06-16 22:01:50 -0700},
	Date-Modified = {2007-06-16 22:31:35 -0700},
	Journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/rockfish_DLM/caddy_refpoint.pdf},
	Pages = {1307-1324},
	Title = {Current usage of fisheries indicators and reference points, and their potential application to management of fisheries for marine invertebrates},
	Volume = {61},
	Year = {2004}}

@article{gibson_est_refpoint,
	Author = {Jamie, A. and Gibson, F. and Myers, Ransom A.},
	Date-Added = {2007-06-16 22:00:34 -0700},
	Date-Modified = {2007-06-16 22:01:39 -0700},
	Journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/rockfish_DLM/gibson_est_refpoint.pdf},
	Pages = {1771-1783},
	Title = {Estimating reference fishing mortality rates from noisy spawner-recruit data},
	Volume = {61},
	Year = {2004}}

@article{collie_refpoint,
	Annote = {Ha! 'When the life-history parameters change over time, the BRP's become moving targets. In particular, the natural mortality of prey species depends on predator levels; conversely, predator growth rates depend on prey ability.'

It's probably safe to just cite Caddy and Mahon as supporting indicators rather than targets.},
	Author = {Collie, Jeremy S. and Gislason, Henrik},
	Date-Added = {2007-06-16 21:59:09 -0700},
	Date-Modified = {2007-06-16 22:37:51 -0700},
	Journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/rockfish_DLM/collie_refpoint.pdf},
	Pages = {2167-2176},
	Title = {Biological reference points for fish stocks in a multispecies context},
	Volume = {58},
	Year = {2001}}

@article{murawski_dem_variation,
	Annote = {Spawning stock biomass alone isn't enough to predict recruitment, you need to take into account maternal size, age and experience. Demographic shifts can make a difference that's hard to see if you just fit analytical SR models.},
	Author = {Murawski, S. A. and Rago, P. J. and Trippel, E. A.},
	Date-Added = {2007-06-16 21:57:43 -0700},
	Date-Modified = {2007-06-16 22:12:26 -0700},
	Journal = {ICES Journal of Marine Science},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/rockfish_DLM/murawski_dem_variation.pdf},
	Pages = {1002-1014},
	Title = {Impacts of demographic variation in spawning characteristics on reference points for fishery management},
	Volume = {58},
	Year = {2001}}

@article{heino,
	Author = {Heino, Mikko},
	Date-Added = {2007-06-16 13:42:46 -0700},
	Date-Modified = {2007-06-16 13:42:46 -0700},
	Journal = {Canadian Journal of Fisheries and Aquatic Sciences},
	Local-Url = {file://localhost/Users/anand/Desktop/decades_of_research/RPViewDoc},
	Pages = {1971-1982},
	Title = {Management of Evolving Fish Stocks},
	Volume = {55},
	Year = {1998}}

@article{hunter_2004,
	Author = {Hunter, Christine M. and Runge, Michael C.},
	Date-Added = {2007-06-16 13:42:46 -0700},
	Date-Modified = {2007-06-16 13:42:46 -0700},
	Journal = {Journal of Wildlife Management},
	Local-Url = {file://localhost/Users/anand/Desktop/decades_of_research/i0022-541X-68-3-585.pdf},
	Number = {3},
	Pages = {585-594},
	Title = {The importance of environmental variability and management control error to optimal harvest policies},
	Volume = {68},
	Year = {2004}}

@article{kirkwood_1981,
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	Date-Added = {2007-06-16 13:42:46 -0700},
	Date-Modified = {2007-06-16 13:42:46 -0700},
	Journal = {Mathematical Biosciences},
	Local-Url = {file://localhost/Users/anand/Desktop/decades_of_research/sdarticle.pdf},
	Pages = {119-129},
	Title = {Allowing for risks in setting catch limits based on {MSY}},
	Volume = {53},
	Year = {1981}}

@article{mace_2001,
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	Date-Added = {2007-06-16 13:42:46 -0700},
	Date-Modified = {2007-06-16 13:42:46 -0700},
	Journal = {Fish and fisheries},
	Local-Url = {file://localhost/Users/anand/Desktop/decades_of_research/j%252E1467-2979%252E2001%252E00033%252Ex.pdf},
	Pages = {2-32},
	Title = {A new role for {MSY} in single-species and ecosystem approaches to fisheries stock assessment and management},
	Volume = {2},
	Year = {2001}}

@article{murawski_1989,
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	Date-Added = {2007-06-16 13:42:46 -0700},
	Date-Modified = {2007-06-16 13:42:46 -0700},
	Journal = {Transnactions of the American Fisheries Society},
	Local-Url = {file://localhost/Users/anand/Desktop/decades_of_research/i1548-8659-118-4-349.pdf},
	Number = {4},
	Pages = {349-367},
	Title = {Yield sustainability under constant-catch policy and stochastic recruitment},
	Volume = {118},
	Year = {1989}}

@article{ryan_1986,
	Author = {Ryan, Dennis and Hanson, Floyd B.},
	Date-Added = {2007-06-16 13:42:46 -0700},
	Date-Modified = {2007-06-16 13:42:46 -0700},
	Journal = {Journal of mathematical biology},
	Local-Url = {file://localhost/Users/anand/Desktop/decades_of_research/fulltext.pdf},
	Pages = {259-277},
	Title = {Optimal harvesting of a logistic population in an environment with stochastic jumps},
	Volume = {24},
	Year = {1986}}

@article{sissenwine_1978,
	Author = {Sissenwine, Michael P.},
	Date-Added = {2007-06-16 13:42:46 -0700},
	Date-Modified = {2007-06-16 13:42:46 -0700},
	Journal = {Fisheries},
	Local-Url = {file://localhost/Users/anand/Desktop/decades_of_research/Sissenwine_1978.pdf},
	Number = {6},
	Pages = {22-42},
	Title = {Is {MSY} an adequate foundation for optimum yield?},
	Volume = {3},
	Year = {1978}}

@article{aitsahalia,
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	Date-Added = {2007-06-14 16:15:38 -0700},
	Date-Modified = {2007-06-29 13:29:45 -0700},
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	Year = {2007}}

@article{Larkin,
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	Date-Added = {2007-06-02 18:38:41 -0700},
	Date-Modified = {2007-06-16 23:24:08 -0700},
	Journal = {Transactions of the American Fisheries Society},
	Local-Url = {file://localhost/Users/anand/Desktop/decades_of_research/larkin.pdf},
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	Number = {1},
	Pages = {1-11},
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	Volume = {106},
	Year = {1977}}

@book{herbie,
	Author = {Ferreira, Marco A. R. and Lee, Herbert K. H.},
	Date-Added = {2007-03-05 20:52:43 -0800},
	Date-Modified = {2007-03-05 20:53:30 -0800},
	Publisher = {Springer},
	Title = {Multiscale modeling: a {B}ayesian perspective},
	Year = {2007}}

@book{scheduling,
	Author = {Dandamundi, Shivarama},
	Date-Added = {2007-03-05 20:08:53 -0800},
	Date-Modified = {2007-03-05 20:09:59 -0800},
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	Year = {2003}}

@inproceedings{bayesian_logic,
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	Date-Modified = {2007-03-05 12:30:20 -0800},
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	Url = {citeseer.ist.psu.edu/kersting00bayesian.html},
	Year = {2000}}

@book{jensen,
	Author = {Jensen, Finn V.},
	Date-Added = {2007-03-05 12:23:56 -0800},
	Date-Modified = {2007-03-05 12:24:35 -0800},
	Publisher = {Springer},
	Title = {Bayesian networks and decision graphs},
	Year = {2001}}

@book{ppp,
	Author = {Chalmers, Alan and Tidmus, Jonathan},
	Date-Added = {2007-03-05 12:20:07 -0800},
	Date-Modified = {2007-03-05 12:21:42 -0800},
	Publisher = {International Thomson Computer Press},
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	Year = {1996}}

@article{stochastic_monads,
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	Author = {Norman Ramsey and Avi Pfeffer},
	Doi = {http://doi.acm.org/10.1145/565816.503288},
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	Journal = {SIGPLAN Not.},
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	Publisher = {ACM Press},
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	Volume = {37},
	Year = {2002}}

@inproceedings{IBAL,
	Author = {Avi Pfeffer},
	Booktitle = {{IJCAI}},
	Date-Modified = {2007-03-05 11:34:15 -0800},
	Pages = {733-740},
	Title = {{IBAL}: A Probabilistic Rational Programming Language},
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	Year = {2001}}

@book{sampling_functions,
	Author = {Park, Sungwoo and Pfenning, Frank and Thrun, Sebastian},
	Date-Added = {2007-03-05 11:31:49 -0800},
	Date-Modified = {2007-03-05 11:32:39 -0800},
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	Year = {2005}}

@inproceedings{Yonezawa,
	Author = {Yonezawa, Akinori and Briot, Jean-Pierre and Shibayama, Etsuya},
	Booktitle = {Proceedings of Object-Oriented Programming Systems, Languages and Applications Conference},
	Date-Added = {2007-03-01 20:09:59 -0800},
	Date-Modified = {2007-03-01 20:12:48 -0800},
	Number = {11},
	Organization = {Association for Computing Machinery, Inc.},
	Pages = {258-268},
	Series = {{SIGPLAN} Notices},
	Title = {Object-oriented concurrent programming in {ABCL/1}},
	Volume = {21},
	Year = {1986}}

@article{Agha,
	Author = {Agha, Gul and Fr{\o}lund, Svend and Kim, Woo Young},
	Date-Added = {2007-03-01 20:08:35 -0800},
	Date-Modified = {2007-03-01 20:14:46 -0800},
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	Month = {May},
	Number = {2},
	Pages = {3-14},
	Title = {Abstraction and modularity mechanisms for concurrent computing},
	Volume = {1},
	Year = {1993}}

@article{Hudak,
	Author = {Hudak, Paul},
	Date-Added = {2007-03-01 20:07:51 -0800},
	Date-Modified = {2007-03-01 20:08:31 -0800},
	Journal = {Computer},
	Month = {August},
	Number = {8},
	Pages = {60-70},
	Title = {Para-Functional Programming},
	Volume = {19},
	Year = {1986}}

@webpage{PyMC,
	Date-Added = {2007-02-24 18:25:41 -0800},
	Date-Modified = {2007-02-24 18:25:58 -0800},
	Url = {www.trichech.us/PyMC}}

@article{kuangberetta,
	Author = {Kuang, Yang and Beretta, Edoardo},
	Date-Added = {2007-02-24 17:35:28 -0800},
	Date-Modified = {2007-02-24 17:36:11 -0800},
	Journal = {Journal of Mathematical Biology},
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	Volume = {36},
	Year = {1998}}

@article{holling_resilience,
	Author = {Holling, C. S.},
	Date-Added = {2007-02-24 17:33:15 -0800},
	Date-Modified = {2007-02-24 17:34:35 -0800},
	Journal = {Annual Review of Ecology and Systematics},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/Qual/docs/Holling.pdf},
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	Title = {Resilience and stability of ecological systems},
	Volume = {4},
	Year = {1973}}

@unpublished{platform_2015,
	Author = {Borkar, Shekhar Y. and Dubey, Pradeep and Kahn, Kevin C. and Kuck, David J. and Mulder, Hans and Pawlowski, Stephen S. and Rattner, Justin R.},
	Date-Added = {2007-02-24 17:28:22 -0800},
	Date-Modified = {2007-02-24 17:31:27 -0800},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/Qual/docs/Platform_2015.pdf},
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@article{abrams_ratio,
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	Date-Added = {2007-02-24 17:27:18 -0800},
	Date-Modified = {2007-02-24 17:38:42 -0800},
	Journal = {Ecology},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/Qual/docs/Abrams_Ratiodependent.pdf},
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	Pages = {1842-1850},
	Title = {The fallacies of ``ratio-dependent" predation},
	Volume = {75},
	Year = {1994}}

@article{levin_scaling,
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	Date-Added = {2007-02-24 17:23:53 -0800},
	Date-Modified = {2007-02-24 17:25:23 -0800},
	Journal = {Ecology letters},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/Qual/docs/Weitz_Levin_Scaling.pdf},
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	Title = {Size and scaling of predator-prey dynamics},
	Volume = {9},
	Year = {2006}}

@article{Dorazio,
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	Date-Added = {2007-01-11 08:17:35 -0800},
	Date-Modified = {2007-01-11 08:18:36 -0800},
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	Pages = {556-563},
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	Volume = {13},
	Year = {2003}}

@article{Wikle,
	Author = {Wikle, C. K.},
	Date-Added = {2007-01-11 05:12:37 -0800},
	Date-Modified = {2007-01-11 05:13:33 -0800},
	Journal = {Ecology},
	Number = {2},
	Pages = {1382-1394},
	Title = {Heirarchical {B}ayesian models for predicting the spread of ecological processes},
	Volume = {86},
	Year = {2003}}

@article{Wu,
	Author = {Wu, J. and Fukuhara, M. and Takeda, T.},
	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2007-02-24 17:26:28 -0800},
	Journal = {Ecological Modeling},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/Qual/docs/stupid_neuralnet.pdf},
	Pages = {289-304},
	Title = {Parameter estimation of an ecological system by a neural network with residual minimization training},
	Year = {189}}

@article{WoodThomas,
	Author = {Wood, S. N. and Thomas, M. B.},
	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2007-02-26 08:59:17 -0800},
	Journal = {Proceedings of the Royal Society B},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/Qual/docs/wood_thomas_supersensitivity.pdf},
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	Title = {Super sensitivity to structure in biological models},
	Volume = {266},
	Year = {1999}}

@article{Wood94,
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	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2006-12-12 14:41:16 -0500},
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	Year = {1994}}

@article{Volterra,
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	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2006-12-12 14:41:16 -0500},
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	Volume = {2},
	Year = {1926}}

@book{Nisbet,
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	Author = {Nisbet, R. M. and Gurney, W. S. C.},
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	Date-Modified = {2006-12-12 14:41:16 -0500},
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	Year = {1982}}

@book{Lotka,
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	Author = {Lotka, A. J.},
	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2006-12-12 14:41:16 -0500},
	Publisher = {Williams and Wilkins},
	Title = {Elements of physical biology},
	Year = {1925}}

@article{JostArditi,
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	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2006-12-12 14:41:16 -0500},
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	Pages = {229-243},
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	Year = {2001}}

@article{Jessop,
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	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2006-12-12 14:41:16 -0500},
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	Pages = {189-197},
	Title = {Big questions, small worlds: microbial model systems in ecology},
	Volume = {19},
	Year = {2005}}

@article{Jeschke,
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	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2006-12-12 14:41:16 -0500},
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	Title = {Predator functional responses: Discriminating between handling and digesting prey},
	Volume = {72},
	Year = {2002}}

@article{Holling,
	Author = {Holling, C. S.},
	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2006-12-12 14:41:16 -0500},
	Journal = {The Canadian Entomologist},
	Pages = {385-398},
	Title = {Some characteristics of simple types of predation and parasitism},
	Volume = {91},
	Year = {1959}}

@article{Hassell,
	Author = {Hassell, M. P. and Varley, G. C.},
	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2007-02-24 17:35:08 -0800},
	Journal = {Nature},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/Qual/docs/hassell_varley_inductive.pdf},
	Pages = {1133-1137},
	Title = {New inductive population model for insect parasites and its bearing on biological control},
	Volume = {223},
	Year = {1969}}

@article{Harrison,
	Author = {Harrison, G. W.},
	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2007-02-24 17:35:20 -0800},
	Journal = {Ecology},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/Qual/docs/harrison_luckinbill.pdf},
	Pages = {357-374},
	Title = {Comparing predator-prey models to {L}uckinbill's experiment with {{\em P}}{\em aramecium} and {{\em D}}{\em idinium}},
	Volume = {76},
	Year = {1995}}

@article{Ginzburg,
	Author = {Ginzburg, L. R. and Ak{\c c}akaya, H. R.},
	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2007-08-20 16:04:25 -0700},
	Journal = {Ecology},
	Pages = {1536-1543},
	Title = {Consequences of ratio-dependent predation for steady-state properties of systems},
	Volume = {73},
	Year = {1992}}

@book{Gause,
	Address = {Baltimore},
	Author = {Gause, G. F.},
	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2006-12-12 14:41:16 -0500},
	Publisher = {Williams and Wilkins},
	Title = {The struggle for existence},
	Year = {1934}}

@article{Ellner,
	Author = {Ellner, S. P. and Seifu, Y. and Smith, R. H.},
	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2007-02-24 17:36:40 -0800},
	Journal = {Ecology},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/Qual/docs/ellner_gradient_matching.pdf},
	Pages = {2256-2270},
	Title = {Fitting population dynamic models to time-series data by gradient matching},
	Volume = {83},
	Year = {2002}}

@article{DeAngelis,
	Author = {De{A}ngelis, D. L. and Goldstein, R. A. and O{'N}eill, R. V.},
	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2007-02-24 17:38:55 -0800},
	Journal = {Ecology},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/Qual/docs/a_model.pdf},
	Pages = {881-892},
	Title = {A model for trophic interaction},
	Volume = {56},
	Year = {2002}}

@article{Beddington,
	Author = {Beddington, J. R.},
	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2006-12-12 14:41:16 -0500},
	Journal = {Journal of Animal Ecology},
	Pages = {331-340},
	Title = {Mutual interference between parasites or predators and its effect on searching efficiency},
	Volume = {44},
	Year = {1975}}

@article{Arditi,
	Author = {Arditi, R. and Ginzburg, L. R.},
	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2006-12-12 14:41:16 -0500},
	Journal = {Journal of Theoretical Biology},
	Pages = {311-326},
	Title = {Coupling in predator-prey dynamics: Ratio-dependence},
	Volume = {139},
	Year = {1989}}

@article{Akcakaya,
	Author = {Akcakaya, H. R. and Arditi, R. and Ginsburg, L. R.},
	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2007-06-29 14:15:29 -0700},
	Journal = {Ecology},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/Qual/docs/akcakaya_arditi_ginzburg.pdf},
	Pages = {995-1004},
	Title = {Ratio-dependent predation: an abstraction that works},
	Volume = {76},
	Year = {1995}}

@article{AbramsGinzburg,
	Author = {Abrams, P. A. and Ginzburg, L. R.},
	Date-Added = {2006-12-12 14:41:16 -0500},
	Date-Modified = {2007-02-27 11:31:53 -0800},
	Journal = {TREE},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/Qual/docs/abrams_ginzburg.pdf},
	Pages = {337-341},
	Title = {The nature of predation: prey dependent, ratio dependent, or neither?},
	Year = {2000}}

@book{Mirowski,
	Author = {Mirowski, Philip},
	Date-Added = {2006-11-30 18:12:01 -0800},
	Date-Modified = {2007-06-29 14:19:45 -0700},
	Publisher = {Cambridge University Press},
	Title = {More heat than light},
	Year = {1991}}

@article{lorenzen_1996,
	Author = {Lorenzen, Kai},
	Date-Added = {2006-11-28 13:41:35 -0800},
	Date-Modified = {2006-11-28 13:43:02 -0800},
	Pages = {627-647},
	Publisher = {Journal of Fish Biology},
	Title = {The relationship between body weight and natural mortality in juvenile and adult fish: a comparison of natural ecosystems and aquaculture},
	Volume = {49},
	Year = {1996}}

@article{Beskos,
	Author = {Beskos, Alexandros and Papaspiliopolous, Omiros and Roberts, Gareth O. and Fearnhead, Paul},
	Date-Added = {2006-11-28 13:23:30 -0800},
	Date-Modified = {2007-06-14 16:10:58 -0700},
	Journal = {Journal of the Royal Statistical Society Series B},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/math/MCMC_tricks/beskos.pdf},
	Pages = {333-382},
	Title = {Exact and computationally efficient likelihood-based estimation for discretely-observed diffusion processes},
	Volume = {68},
	Year = {2006}}

@article{Hoeting,
	Author = {Hoeting, Jennifer A. and Madigan, David and Raftery, Adrian and Volinsky, Chris T.},
	Date-Added = {2006-11-28 13:23:30 -0800},
	Date-Modified = {2006-11-28 13:23:30 -0800},
	Journal = {Statistical Science},
	Number = {4},
	Pages = {382-417},
	Title = {Bayesian model averaging: a tutorial},
	Volume = {14},
	Year = {1999}}

@book{Kingsland,
	Author = {Kingsland, Sharon},
	Date-Added = {2006-11-28 13:23:30 -0800},
	Date-Modified = {2006-11-28 13:23:30 -0800},
	Edition = {Second},
	Publisher = {The University of Chicago Press},
	Title = {Modeling Nature},
	Year = {1995}}

@book{Shreve,
	Author = {Shreve, Steven E.},
	Date-Added = {2006-11-28 13:23:30 -0800},
	Date-Modified = {2006-11-28 13:23:30 -0800},
	Publisher = {Springer},
	Title = {Stochastic calculus for finance: Continuous time models},
	Year = {2004}}

@book{youngson_1996,
	Author = {youngson, a. and hay, d.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Publisher = {swan hill press},
	Title = {the lives of salmon},
	Year = {1996}}

@article{ward_1988,
	Author = {ward, b. r. and slaney, p. a.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Canadian Journal of fisheries and aquatic sciences},
	Pages = {1110-1122},
	Title = {life history and smolt-to-adult survival of {K}eogh river steelhead trout {{\em S}}{\em almo gairdneri} and the relationship to smolt size},
	Volume = {45},
	Year = {1988}}

@article{thorpe_1989,
	Author = {Adams, C. E. and Thorpe, J. E.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Aquaculture},
	Pages = {403-409},
	Title = {Photoperiod and temperature effects on early development and reproductive investment in the {A}tlantic salmon ({{\em S}}{\em almo salar L.}},
	Volume = {79},
	Year = {1989}}

@article{alvarez_2005,
	Author = {Alvarez, D. and Nicieza, A. G.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Proceedings of the Royal Society of London B.},
	Pages = {601-607},
	Title = {Compensatory response `defends' energy levels but not growth trajectories in brown trout, {{\em S}}{\em almo trutta L.}},
	Volume = {272},
	Year = {2005}}

@article{beckman_2000,
	Author = {Beckman, B. R. and Larsen, D. A. and Sharpe, C. and Lee-Pawlak, B. and Schreck, C. B. and Dickoff, W. W.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Transactions of the American Fisheries Society},
	Pages = {727-753},
	Title = {Physiological status of naturally reared juvenile spring chinook salmon in the {Y}akima {R}iver: Seasonal dynamics and changes associated with smolting},
	Volume = {129},
	Year = {2000}}

@article{Beckman1998,
	Author = {Beckman, B. R. and Dickoff, W. W.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Journal of Fish Biology},
	Pages = {808-826},
	Title = {Plasticity of smolting in spring chinook salmon: relation to growth and insulin-like growth factor-I},
	Volume = {53},
	Year = {1998}}

@techreport{bley_1988,
	Author = {Bley, P. W. and Moring, J. R.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Institution = {Fish and Wildlife Service, {US} Department of the Interior},
	Number = {88(9)},
	Title = {Freshwater and Ocean Survival of {A}tlantic Salmon and Steelhead: A Synopsis},
	Type = {Report},
	Year = {1988}}

@article{blurns_1971,
	Author = {Blurns, J. W.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Institution = {California Fish and Game},
	Journal = {California Fish and Game},
	Pages = {44-57},
	Title = {The carrying capacity for juvenile salmonids in some northern {C}alifornia streams},
	Volume = {57},
	Year = {1971}}

@book{clark_2000,
	Author = {Clark, C. W. and Mangel, M.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {O},
	Publisher = {Oxford University Press},
	Title = {Dynamic state variable models in ecology: methods and applications},
	Year = {2000}}

@article{giger_2006,
	Author = {Giger, T. and Excoffer, L. and Day, P. J. R. and Champigneulle, A. and Hansen, M. M. and Powell, R. and Largiader, C. R.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Current Biology},
	Pages = {281-282},
	Title = {Life history shapes gene expression in salmonids},
	Volume = {16},
	Year = {2006}}

@article{gross_1985,
	Author = {Gross, M. R.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Nature},
	Pages = {47-48},
	Title = {Disruptive selection for alternative life histories in salmon},
	Volume = {313},
	Year = {1985}}

@article{hager_1976,
	Author = {Hager},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800}}

@article{hilborn_1993,
	Author = {Hilborn, R. and Winton, J.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Canadian Journal of fisheries and aquatic sciences},
	Pages = {2043-2056},
	Title = {Learning to enhance salmon production: lessons from the salmonid enhancement program.},
	Volume = {50},
	Year = {1993}}

@article{hoar_1976,
	Author = {Hoar, W. S.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Journal of the fisheries research board of canada},
	Pages = {1233-1252},
	Title = {Smolt transformation: evolution, behavior and physiology},
	Volume = {33},
	Year = {1976}}

@book{houston_199,
	Author = {Houston, A. I. and McNamara, J. M.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Publisher = {Cambridge University Press},
	Title = {Models of adaptive behavior},
	Year = {1999}}

@article{hutchings_1994,
	Author = {Hutchings, J. A. and Myers, R. A.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Evolutionary ecology},
	Pages = {256-268},
	Title = {The evolution of alternative mating strategies in variable environments},
	Volume = {8},
	Year = {1994}}

@book{jobling_1994,
	Author = {Jobling, M.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Publisher = {Chapman \& Hall},
	Title = {Fish bioenergetics},
	Year = {1994}}

@article{koseki_2006,
	Author = {Koseki, Y. and Fleming, I. A.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Journal of animal ecology},
	Pages = {445-455},
	Title = {Spatio-temporal dynamics of alternative male phenotypes in coho salmon populations in response to ocean environment},
	Volume = {75},
	Year = {2006}}

@techreport{kubo_1980,
	Author = {Kubo, T.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:20:27 -0800},
	Institution = {{H}okkaido salmon hatchery},
	Number = {34},
	Title = {Studies on the life history of the ``{M}asu" salmon ({{\em O}}{\em nchorhynchus masou}) in {H}okkaido},
	Type = {Scientific report},
	Year = {1980}}

@article{langdon_1985,
	Author = {Langdon, J. S. and Thorpe, J. E.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {L. Aquaculture},
	Pages = {83-95},
	Title = {The ontogeny of smoltification: developmental patterns of gill {N}a+/{K}+/{ATP}ase, {SDH} and chloride cells in juvenile {A}tlantic salmon, {{\em S}}{\em almo salar}},
	Volume = {45},
	Year = {1985}}

@article{larsen_2004,
	Author = {Larsen, D. A. and Beckman, B. R. and Cooper, K. A. and Barrett, D. and Johnston, M. and Swanson, P. and Dickoff, W. W.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Transactions of the American Fisheries Society},
	Pages = {98-120},
	Title = {Assessment of high rates of precocious male maturation in a spring chinook salmon supplementation hatchery program},
	Volume = {133},
	Year = {2004}}

@book{levin_1999,
	Author = {Levin, S.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Publisher = {Helix books},
	Title = {Fragile dominion: complexity and the commons},
	Year = {1999}}

@article{mangel_2005,
	Author = {Mangel, M. and Munch, S. B.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {American naturalist},
	Pages = {E155-E176},
	Title = {A life-history perspective on short- and long- term consequences of compensatory growth},
	Volume = {166},
	Year = {2005}}

@article{mangel_1992,
	Author = {Mangel, M. and Ludwig, D.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Annual review of ecology and systematics},
	Pages = {507-536},
	Title = {Definition and evaluation of behavioral and developmental programs},
	Volume = {23},
	Year = {1992}}

@article{mangel_1994,
	Author = {Mangel, M.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Deep sea research, {II} (tropical studies in oceanography)},
	Pages = {75-106},
	Title = {Climate change and salmonid life history variation},
	Volume = {41},
	Year = {1994}}

@article{mcewan_2001,
	Author = {Mc{E}wan, D.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {California Department of Fish and Game Bulletin},
	Pages = {1-43},
	Title = {Central valley steelhead},
	Volume = {179},
	Year = {2001}}

@article{metcalfe_2001,
	Author = {Metcalfe, N. and Monaghan, P.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Trends in ecology and evolution},
	Pages = {245-260},
	Title = {Compensation for a bad start: grow now, pay later?},
	Volume = {16},
	Year = {2001}}

@article{policansky_1983,
	Author = {Policansky, D.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {American zoologist},
	Pages = {57-63},
	Title = {Size, age, and demography of metamorphosis and sexual maturation in fishes},
	Volume = {23},
	Year = {1983}}

@article{railsback_1999,
	Author = {Railsback, S. F. and Rose, K. A.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Transactions of the American Fisheries Society},
	Pages = {241-256},
	Title = {Bioenergetics modeling of stream trout growth: temperature and food consumption effects},
	Volume = {128},
	Year = {1999}}

@article{rikardsen_2004,
	Author = {Rikardsen, A. H. and Thorpe, J. E. and Dempson, J. B.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {ecology of freshwater fish},
	Pages = {305-311},
	Title = {modelling life history-variation of {A}rctic charr},
	Volume = {13},
	Year = {2004}}

@article{shearer_2006,
	Author = {Shearer, K. D. and Parkins, B. and Gadberry, B. and Beckman, B. R. and Swanson, P.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Aquaculture},
	Pages = {545-556},
	Title = {effects of growth rate/body size and a low lipid diet on the incidence of early sexual maturation in juvenile male spring chinook salmon ({{\em O}}{\em nchorhynchus tshawytscha})},
	Volume = {252},
	Year = {2006}}

@article{shearer_2000,
	Author = {Shearer, K. D. and Swanson, P.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Aquaculture},
	Pages = {343-367},
	Title = {the effect of whole body lipid on early sexual maturation of 1{+} age male chinook salmon ({{\em O}}{\em nchorhynchus tshawytscha})},
	Volume = {190},
	Year = {2000}}

@article{smithgill_1983,
	Author = {Smith-Gill, S. J.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {American zoologist},
	Pages = {47-55},
	Title = {Developmental plasticity: conversion versus phenotypic modulation},
	Volume = {23},
	Year = {1983}}

@article{snover_2006,
	Author = {Snover, M. L. and Watters, G. M. and Mangel, M.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {American naturalist},
	Pages = {E140-E157},
	Title = {top-down and bottom-up control of life history strategies in coho salmon ({{\em O}}{\em nchorhynchus kisutch})},
	Volume = {167},
	Year = {2006}}

@article{snover_2005,
	Author = {Snover, M. L. and Watters, G. M. and Mangel, M.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Canadian Journal of fisheries and aquatic sciences},
	Pages = {1219-1230},
	Title = {interacting effects of behavior and oceanograhpy on growth in salmonids with examples for coho salmon ({{\em O}}{\em nchorhynchus kisutch})},
	Volume = {62},
	Year = {2005}}

@book{stearns_1992,
	Author = {Stearns, S. C.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Publisher = {Oxford University Press},
	Title = {the evolution of life histories},
	Year = {1992}}

@article{thorpe_1998,
	Author = {Thorpe, J. E. and Mangel, M. and Metcalfe, N. B. and Huntingford, F. A.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Evolutionary ecology},
	Pages = {581-600},
	Title = {Modeling the proximate basis of life history variation, with application to {A}tlantic salmon, {{\em S}}{\em almo salar} {{\em L.}}},
	Volume = {121},
	Year = {1998}}

@article{thorpe_1994b,
	Author = {Thorpe, J. E.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Aquaculture},
	Pages = {105-113},
	Title = {An alternative view of smolting salmonids},
	Volume = {121},
	Year = {1994}}

@article{thorpe_1994a,
	Author = {Thorpe, J. E.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {aquaculture and fisheries management},
	Pages = {77-87},
	Title = {Reproductive strategies in {A}tlantic salmon, {{\em S}}{\em almo salar} {{\em L}}.},
	Volume = {25},
	Year = {1994}}

@incollection{thorpe_1986,
	Author = {Thorpe, J. E.},
	Booktitle = {Salmonid Age at Maturity},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Editor = {Meerburg, D. J.},
	Pages = {7-14},
	Publisher = {Canadian special publications in fisheries and aquatic sciences},
	Title = {Age at first maturity in {A}tlantic salmon, {{\em S}}{\em almo salar}: freshwater period influences and conflicts with smolting},
	Volume = {89},
	Year = {1986}}

@inproceedings{thorpe_1982,
	Author = {Thorpe, J. E.},
	Booktitle = {proceedings of the salmon and trout migratory behavior symposium},
	Chapter = {migration in salmonids with special reference to juvenile movements in freshwater},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Editor = {Brannon, E. L. and Salo, E. O.},
	Organization = {University of {W}ashington, {S}eattle},
	Pages = {86-97},
	Title = {1982},
	Year = {1982}}

@article{tinbergen_1963,
	Author = {Tinbergen, N.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Zeitschrift fr Tierpsychologie},
	Pages = {410-433},
	Title = {On aims and methods of ethology},
	Volume = {20},
	Year = {1963}}

@article{vandenberghe_1989,
	Author = {{v}an den {B}erghe, E. P. and Gross, M. R.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {evolution},
	Pages = {125-140},
	Title = {natural selection resulting from female breeding competition in {P}acific salmon (coho: {{\em O}}{\em nchorhynchus kisutch})},
	Volume = {43},
	Year = {1989}}

@article{vandenberghe_1986,
	Author = {{v}an den {B}erghe, E. P. and Gross, M. R.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Canadian Journal of fisheries and aquatic sciences},
	Pages = {204-206},
	Title = {length of breeding life of coho salmon {{\em O}}{\em nchorhynchus kisutch}},
	Volume = {41},
	Year = {1984}}

@article{vandenberghe_1984,
	Author = {{v}an den {B}erghe, E. P. and Gross, M. R.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Canadian Journal of fisheries and aquatic sciences},
	Pages = {204-206},
	Title = {Female size and nest depth in coho salmon {{\em O}}{\em chorhynchus kisutch}},
	Volume = {41},
	Year = {1984}}

@article{west_1997,
	Author = {West, G. B. and Brown, J. H. and Enquist, B. J.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:18:05 -0800},
	Journal = {Science},
	Pages = {122-126},
	Title = {A general model for the origin of allometric scaling laws in biology},
	Volume = {276},
	Year = {1997}}

@book{West,
	Address = {New York},
	Author = {West, M. and Harrison, J.},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2007-06-16 21:57:33 -0700},
	Publisher = {Springer},
	Series = {Springer Series in Statistics},
	Title = {Bayesian Forecasting and Dynamic Modeling},
	Year = {1997}}

@book{mangel_2006,
	Author = {Mangel, Marc},
	Date-Added = {2006-11-28 13:18:05 -0800},
	Date-Modified = {2006-11-28 13:43:48 -0800},
	Publisher = {Cambridge University Press},
	Title = {The theoretical biologist's toolbox},
	Year = {2006}}

@book{Strogatz,
	Author = {Strogatz, Steven H.},
	Date-Added = {2006-09-28 11:28:02 -0700},
	Date-Modified = {2007-06-29 14:28:18 -0700},
	Publisher = {Perseus Books},
	Title = {Nonlinear dynamics and chaos: with applications to physics, biology, chemistry, and engineering},
	Year = {1994}}

@book{Moller,
	Author = {M{\o }ller, Jesper and Waagepetersen, Rasmus Plenge},
	Date-Added = {2006-09-28 11:25:44 -0700},
	Date-Modified = {2007-08-20 14:16:57 -0700},
	Publisher = {Chapman {\&} Hall {/} CRC},
	Series = {Monographs on Statistics and Applied Probability},
	Title = {Statistical inference and simulation for spatial point processes},
	Year = {2003}}

@article{fujiwara,
	Author = {Fujiwara, Masami and Kendall, Bruce and Nisbet, Roger M. and Bennett, William A.},
	Date-Added = {2006-08-29 08:55:06 -0700},
	Date-Modified = {2006-08-29 09:03:48 -0700},
	Journal = {Ecology},
	Keywords = {steelhead},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/steelhead/fujiwaraplus05.pdf},
	Number = {6},
	Pages = {1441-1451},
	Title = {Analysis of size trajectory data using an energetic-based growth model},
	Volume = {86},
	Year = {2005}}

@article{Skalski,
	Author = {Skalski, Garrick T. and Picha, Matthew E. and Gilliam, James F. and Borski, Russel J.},
	Date-Added = {2006-08-29 08:52:56 -0700},
	Date-Modified = {2006-08-29 09:06:07 -0700},
	Journal = {Ecology},
	Keywords = {Steelhead},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/steelhead/Skalski%20et%20al%202005.pdf},
	Number = {6},
	Pages = {1452-1462},
	Title = {Variable intake, compensatory growth, and increased growth efficiency in fish: models and mechanisms},
	Volume = {86},
	Year = {2005}}

@article{rainbow_gut,
	Author = {Pirhonen, Juhani and Koskela, Julia},
	Date-Added = {2006-08-29 08:51:20 -0700},
	Date-Modified = {2006-08-29 09:11:23 -0700},
	Journal = {Aquaculture Research},
	Keywords = {Steelhead},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/steelhead/RainbowStomachContents.pdf},
	Pages = {851-856},
	Title = {Indirect estimation of stomach volume of rainbow trout {{\em O}}{\em ncorhynchus mykiss} ({W}albaum)},
	Volume = {26},
	Year = {2005}}

@book{Abramowitz,
	Address = {New York},
	Date-Modified = {2007-06-29 14:16:19 -0700},
	Editor = {Abramowitz, Milton and Stegun, Irene A.},
	Keywords = {math, special functions, two_species_FR},
	Publisher = {Dover Publications, Inc.},
	Title = {Handbook of mathematical functions},
	Year = {1972}}

@article{Abrams,
	Author = {Abrams, P. A.},
	Date-Modified = {2007-06-29 14:13:39 -0700},
	Journal = {Annual Review of Ecology and Systematics},
	Keywords = {predator-prey, functional response, dynamical systems, two_species_FR},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/Qual/docs/abrams.pdf},
	Pages = {79-105},
	Title = {The evolution of predator-prey interactions: theory and evidence},
	Volume = {31},
	Year = {2000}}

@book{Banerjee,
	Address = {New York},
	Author = {Banerjee, Sudipto and Carlin, Bradley P. and Gelfand, Alan},
	Date-Modified = {2006-08-29 09:23:04 -0700},
	Keywords = {spatial statistics, gaussian processes, two_species_FR},
	Publisher = {Chapman \& Hall CRC},
	Series = {Monographs on Statistics and Applied Probability},
	Title = {Hierarchical modeling and analysis for spatial data},
	Year = {2004}}

@phdthesis{Beal,
	Author = {Beal, M. J.},
	Date-Modified = {2006-08-29 09:23:20 -0700},
	Keywords = {variational methods, MCMC, two_species_FR, bayesian},
	School = {University College},
	Title = {Variational Algorithms for Approximate Bayesian Inference},
	Type = {PhD},
	Year = {2003}}

@book{Burden,
	Address = {Boston},
	Author = {Burden, Richard L. and Faires, J. Douglas},
	Date-Modified = {2006-08-29 09:19:21 -0700},
	Edition = {7},
	Keywords = {numerical analysis, numerical methods},
	Publisher = {Brooks Cole},
	Title = {Numerical Analysis},
	Year = {2000}}

@article{Chorin,
	Author = {Chorin, Alexandre J. and Krause, Paul},
	Date-Modified = {2006-08-29 09:21:23 -0700},
	Journal = {Proceedings of the National Academy of Sciences},
	Keywords = {brownian motion, SDE, diffusion, MCMC, dynamical systems},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/math/chorinfluidmcmc/chorin_brownian_dim_redux.ps},
	Number = {42},
	Pages = {15013-15017},
	Title = {Dimensional reduction for a Bayesian filter},
	Volume = {101},
	Year = {2004}}

@article{Creaser,
	Author = {Creaser, E. P. and Perkins, H. C.},
	Date-Modified = {2006-08-29 09:20:32 -0700},
	Journal = {Fishery Bulletin},
	Keywords = {fisheries},
	Pages = {494-508},
	Title = {The distribution, food, and age of juvenile bluefish, {{\em P}}{\em omatomus saltatrix}, in Maine.},
	Volume = {92},
	Year = {1994}}

@article{Dacunha-Castelle,
	Author = {Dacunha-Castelle, D. and Florens-Zmirou, D.},
	Date-Modified = {2007-02-24 17:32:07 -0800},
	Journal = {Stochastics},
	Keywords = {brownian motion, SDE, MCMC, dynamical systems},
	Local-Url = {file://localhost/Users/anand/Documents/renearch/Thesis/Qual/docs/NewFokkerPlanckSolution.pdf},
	Pages = {263-284},
	Title = {Estimation of the coefficients of a diffusion from discrete observations},
	Volume = {19},
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@article{Elerian,
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